[R] labels and counting

[dax42]

Hello,

I have got the following problem:
given is a large string sequence consisting of the four letters "A" "C" 
"G" and "T" (as before). Additionally, I have got a second string 
sequence of the same length giving a label for each character. The 
labels are "+" and "-".

Now I would like to create an 8x8 matrix which contains the numbers on 
how often we see all possible pairwise combinations, for example "A" 
with the label "+" followed by "C" with the label "+" or "T"->"C" with 
the labels "-"->"+" etc.

Of course I can just use loops to "walk" along the sequence, but as you 
have shown me so much better solutions in response to my last mail, I 
thought you might be able to help and improve my R skills even further 
..

Thanks for your ideas!
Cheers, Winnie